By assigning to the whole hash, you're overwriting it for each line. 
%hash = (key => 'value'); # Removes previous contents of %hash.

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Assign just to the value corresponding to a key: 

$hash{key} = 'value';

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In your case, it's 

$code{$2} = $1;
$code{$3} = $1;
...

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Update:

Also, [\w] can be written as just \w . Using /i only make sense if your regex contains letters, yours only contains \w and '\s'. Moreover, you can probably simplify the whole program (I'm just guessing as you haven't provided any sample data) to 

while (my $line = <READ>) {
    my ($acid, @codons) = split ' ', $line;
    $code{$_} = $acid for @codons;
}

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($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

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In reply to Re: reading RNA codons into hash by choroba
in thread reading RNA codons into hash by ic23oluk

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